Highly Infectious Nucleic Acid Molecules from Pepper Mottle Virus and Plant Viral Vector Derived from the Same

ABSTRACT

The present invention relates to a plant-infectious nucleic acid molecule from Pepper mottle virus, and a viral vector, a transformed cell and a transgenic plant having it. The present invention first achieves the cloning of the infectious full-length pepper mottle virus cDNA from virus-infected pepper, which enables to perform the molecular biological studies to the infectivity of pepper mottle virus in pepper and tobacco and to provide a plant virus-based vector to highly express a useful foreign protein.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The present invention relates to a plant-infectious nucleic acid molecule from Pepper mottle virus, and a viral vector a transformed cell and a transgenic plant having it.

2. Background of Technique

Various aspects of virus pathogenicity have been studied using in vitro- or in vivo-transcribed infectious RNA derived from full-length cDNA clones. It is not known how virus proteins are expressed from full-length clones, since the vector sequences do not contain promoters expected to transcribe the virus RNA in bacterial cells. Fakhfakh and their colleagues suggested that viral RNA is transcribed from cryptic promoters and protein synthesis initiated at cryptic ribosomal binding sites present in the virus cDNA sequences (Fakhfakh et al., 1996).

However, manipulation and amplification of full-length clones may prove difficult due to instability or toxicity of some virus sequences in bacteria (Chen and Hruening, 1992; Boyer and Haenni, 1994; Fakhfakh et al., 1996). Expression of virus proteins in E. coli has been reported to have toxic effects on the host cells (Lama and Carrasco, 1992; Rodriguez and Shaw, 1991). The toxic effects from undesired protein expression can be relieved by cloning in E. coli strains that reduce the plasmid copy number (Greener, 1993) or using low copy number cloning vectors (Schweizer, 2008).

Among potyviruses, the in vitro synthesis of biologically active RNAs from full-length cDNA clone with bacterial phage promoters have been reported; Tobacco vein mottling virus (TVMV) (Domier et al., 1989; Nicolas et al., 1996), Plum pox virus (PPV) (Riechmann et al., 1990), Zucchini yellow mosaic virus (ZYMV) (Gal-On et al., 1991; Lin et al., 2002), Tobacco etch virus (TEV) (Dolja et al., 1992), Peanut stripe virus (PStV) (Flasinski et al., 1995), Pea seed-borne mosaic virus (PSbMV) (Johansen et al, 1996), Potato virus A (PVA) (Puurand et al., 1996), Papaya ringspot virus (PRSV) (Chiang and Yeh, 1997), Potato virus Y (PVY) (Jakab et al., 1997), Papaya ringspot virus (PRSV) (Chiang and Yeh, 1997), Turnip mosaic virus (TuMV) (Sanchez et al, 1998) and Johnsongrass mosaic virus (JGMV-Jg)(Kim et al., 2003) and so on.

Another system is based on the delivery of particles coated with cDNA or the plasmids directly introduced of a virus into the plant cell to induce infection. In vivo infectious transcripts, which are driven by a Cauliflower mosaic virus (CaMV) 35S promoter that can be transcribed by an endogenous host RNA polymerase, have been reported for PPV-NAT (Maiss et al., 1992), ZYMV (Gal-On et al., 1995), PVY-NTN (Fakhfakh et al., 1996), PSbMV (Johansen, 1996), Clover yellow vein virus (CIYVV) (Takahashi et al, 1997), PRSV (Chiang and Yeh, 1997), PVY-N605 (Jakab et al, 1997), TuMV (Sanchez et al., 1998), Lettuce mosaic virus (LMV) (Yang et al., 1998) and PSbMV-L1 (Olsen and Johansen, 2001). In vitro- or in vivo-transcribed infectious RNA derived from full-length cDNA clones are an important tool in the study of RNA viruses. These clones are possible to facilitated studies of non-destructive monitoring of virus infection without by tagging reporter genes, such as green fluorescence protein gene (GFP) or β-glucuronidase gene (GUS).

Among the potyviruses, TEV was first developed to express reporter gene (Dolja et al., 1992; Carrington et al., 1993). Later, many potyviruses such as PPV (Guo et al., 1998; Fernandez-Fernandez et al., 2001), LMV (German-Retana et al., 2000), CIYVV (Masuta et al., 2000), Wheat streak mosaic virus (WSMV) (Choi et al., 2000), Tobacco vein mottling virus vector (TVMV) (Dietrich and Maiss, 2003), ZYMV (Arazi et al., 2001; Hsu et al., 2004), PVA (Ivanov et al., 2003) and TuMV (Beauchemin et al., 2005) have been engineered into effective expression of reporter gene at different insertion site of virus genome.

Potyviral proteins are expressed by proteolytic processing of the large precursor polyprotein by three virus-encoded proteases, P1, HC-pro and NIa. P1 and HC-pro automatically cleave at their respective C termini, and NIa cleave the remains (Uyeda, 1997). Most of the foreign ORFs are constructed adjacent to the junction between P1 and HC-Pro or NIb and CP by directional insertion. A plant virus-based vector is a useful tool for efficient expression of target foreign proteins in plants. Plant expression systems have a significant advantage compared to other methods of recombinant protein production since plants are much cheaper and easier in cultivation than cell cultures. This system provides rapid and transient expression of heterogonous genes systemically in plants. These virus-based vectors have been used to express genes of pharmaceutical, agronomic value, elicit genetically dominant, gene-silencing phenotypes in plants to determine the functions of unknown genes (Donson et al., 1991; Kumagai et al., 1993, 1995; Masuta et al., 2000; Arazi et al., 2001; Fitzmaurice et at., 2002). They have also been used to produce proteins applicable to various therapeutic interventions and vaccine components that are applicable as therapeutic cancer vaccines (McCormick et al., 1999) Further, expression of sequences in plants by virus expression vectors can result in reprogramming specific metabolic pathways in plants through virus-induced gene-silencing (VIGS) effects (Baulcombe et al., 1999) or protein expression (Fitzmaurice et al., 2002). Heterologous expression of a cDNA for capsanthin-capsorubin synthase (ccs) in N. benthamiana resulted in an orange-red phenotype and the accumulation of novel carotenoids capsanthin and capsorubin (Kumagai et al., 1998).

Throughout this application, various publications and patents are referred and citations are provided in parentheses. The disclosures of these publications and patents in their entities are hereby incorporated by references into this application in order to fully describe this invention and the state of the art to which this invention pertains.

DETAILED DESCRIPTION OF THE INVENTION

The present inventors have made intensive studies to provide a clue to the infectivity of pepper mottle virus (PepMoV) which has pathogenicity to plants, particular pepper and tobacco, and to develop a plant virus vector. As results, we have discovered that the plant virus vector could be constructed, with isolation of highly infectious cDNA of pepper mottle virus and analysis of its base sequence.

Accordingly, it is an object of this invention to provide a pepper mottle virus-derived plant infectious nucleic acid molecule.

It is another object of this invention to provide a recombinant vector including the pepper mottle virus-derived plant infectious nucleic acid molecule.

It is still another object of this invention to provide a cell or a plant transformed by the pepper mottle virus-derived plant infectious nucleic acid molecule.

Other objects and advantages of the present invention will become apparent from the following detailed description together with the appended claims and drawings.

In one aspect of this invention, there is provided a pepper mottle virus-derived plant infectious nucleic acid molecule comprising the nucleotide sequence spanning nucleotides 168 to 9371 of SEQ ID NO:1.

The present inventors have made intensive studies to provide a clue to the infectivity of pepper mottle virus (PepMoV) which has pathogenicity to plants, particular pepper and tobacco, and to develop a plant virus vector. As results, we have discovered that the plant virus vector could be constructed, with isolation of highly infectious cDNA of pepper mottle virus and analysis of its nucleotide sequence and an aphid-uninfected pepper mottle virus vector is newly prepared for blocking a virus infection transfer via aphids using the same.

The present invention first achieves the cloning of the infectious full-length pepper mottle virus cDNA from pepper, which enables to perform the molecular studies to the infectivity of pepper mottle virus and to be used in the preparation of the plant virus-based vector. In addition, the present invention prepares the aphid-uninfected pepper mottle virus-based vector to exclude the transition of virus invasion, contributing to obtaining the plants with highly environmental safety under restricted environments.

The present pepper mottle virus-derived plant infectious nucleic acid molecule includes the nucleotide sequence of SEQ ID NO:1.

The term “nucleic acid molecule” as used herein refers to a deoxyribonucleotide or ribonucleotide polymer (including gDNA, cDNA and mRNA) in either single or double-stranded form, including known analogs of natural nucleotides unless otherwise indicated (Scheit, Nucleotide Analogs, John Wiley, New York (1980); Uhlman and Peyman, Chemical Reviews, 90:543-584 (1990)).

The pepper mottle virus-derived plant highly infectious nucleic acid molecule of this invention has pathogenicity to various plants. Preferably, the present highly infectious nucleic acid molecule exhibits pathogenicity to the genus Nicotiana and Capsicum. More preferably, the present highly infectious nucleic acid molecule exhibits infectivity to Nicotiana benthamiana, Nicotiana tabacum and Capsicum annum.

According to a preferable embodiment, the present nucleic acid molecule further comprises the nucleotide sequence spanning nucleotides 1 to 167 of SEQ ID NO:1.

According to a preferable embodiment, the present nucleic acid molecule further comprises the nucleotide sequence spanning nucleotides 9372 to 9655 of SEQ ID NO:1.

According to a preferable embodiment, the nucleic acid molecule has a substituted nucleotide at nucleotide 9304 of SEQ ID NO:1, in which the substituted nucleotide at nucleotide 9304 is a nucleotide containing A, C or T base.

The term “site-directed mutagenesis” used herein refers to a technique to induce an altered form of one or more specific amino acids by changing one or more specific nucleotides in a cloned gene. The site-directed mutagenesis method is described in Ling et al, “Approaches to DNA mutagenesis: an overview”, Anal Biochem., 254 (2): 157-178 (1997); Dale et al., “Oligonucleotide-directed random mutagenesis using the phosphorothioate method”, Methods Mol. Biol., 57: 369-374 (1996); Smith, “In vitro mutagenesis” Ann. Rev. Genet., 19: 423-462 (1985); Botstein & Shortie, “Strategies and applications of in vitro mutagenesis”, Science, 229: 1193-1201 (1985); Carter, “Site-directed mutagenesis”, Biochem. J., 237: 1-7 (1986); and Kunkel, “The efficiency of oligonucleotide directed mutagenesis”, Nucleic Acids & Molecular Biology (Eckstein, F. and Lilley, D. M. J. eds., Springer Verlag, Berlin (1987)), which are herein incorporated by references. It is also preferable to carry out the present site-directed mutagenesis by PCR method (Ausubel et al., Current Protocols in Molecular Biology, Greene/Wiley Interscience (1987)).

The amino acid substituted by the site-directed mutagenesis in this invention is a portion involved in the aphid infectivity.

According to a conventional study, the aphids missed its infectivity by deleting the amino acids at the N-terminal region of coat protein or by substituting them through site-directed mutagenesis in potyvirus. Particularly, the deletion of Asp-Ala-Gly (DAG) sequence which is a conserved amino acid sequence in potyvirus resulted in the loss of the aphid infectivity (P. L. Atreya et al, Proc. Natl. Acad. Sci., 88: 7887-7891 (1991)).

In another aspect of this invention, there is provided a recombinant vector, comprising (i) the nucleotide sequence as described above, and (ii) a promoter operatively linked to the nucleotide sequence.

The term “operatively linked” refers to functional linkage between a nucleic acid expression control sequence (such as a promoter, signal sequence, or array of transcription factor binding sites) and a second nucleic acid sequence, wherein the expression control sequence affects transcription and/or translation of the nucleic acid corresponding to the second sequence.

The vector system of this invention may be performed by various methods known to those skilled in the art and its practical method is described in Sambrook et al., Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Laboratory Press (2001), which is herein incorporated by reference.

The nucleotide sequences involved in the present vector possessed the most preferable utility since they were isolated from a plant virus and had infectivities to plants. Therefore, the vector of this invention provides a plant expression vector including (i) the pepper mottle virus-derived plant infectious nucleic acid molecule; (ii) a promoter which is operatively linked to the nucleotide sequence of (i) and generates a RNA molecule in plant cells; and (iii) 3′-untranslated region responsible of 3′-terminal polyadenylation of the RNA molecule.

According to a preferable embodiment, the suitable promoter of this invention might include any one commonly used by one ordinarily skilled in the art, for example SP6 promoter, T7 promoter, T3 promoter, PM promoter, maize-ubiquitin promoter, Cauliflower mosaic virus (CaMV)-35S promoter, Nopalin synthase (nos) promoter, Figwort mosaic virus 35S promoter, Sugarcane bacilliform virus promoter, commelina yellow mottle virus promoter, photo-inducible promoter of small subunit of Ribulose-1,5-bis-phosphate carboxylase (ssRUBISCO), cytosolic triosphosphate isomerase (TPI) promoter in rice, adenine phosphoribosyltransferase (APRT) or octopine synthase promoter in Arabidopsis.

Most preferably, the promoter used in the present invention is a bactriophage SP6 promoter. The sequence of bactriophage SP6 promoter is illustrated in SEQ ID NO:5.

According to a preferable embodiment, the suitable 3′-untranslated region responsible of 3′-terminal polyadenylation includes nos 3′-end of nopaline synthase gene of Agrobacterium tumefeciens (Bevan et al., Nucleic Acids Research, 11(2):369-385 (1983)), 3′-end of protease I or II of Agrobacterium tumefeciens, CaMV 35S terminator and the sequence spanning nucleotides 9372 to 9655 of SEQ ID NO:1.

Most preferably, the suitable 3′-untranslated region responsible of 3′-terminal polyadenylation is the sequence spanning nucleotides 9372 to 9655 of SEQ ID NO:1.

Alternatively, the present vector further includes a gene encoding a reporter molecule (example: green fluorescent protein (GFP), yellow fluorescent protein (YFP), red fluorescent protein (RFP), GFP-derived variant protein, luciferase, β-glucuronidase). Most preferably, the present vector further includes a GFP-encoding nucleotide sequence.

Preferably, the GFP-encoding nucleotide sequence is located between NIb and CP cistron of the pepper mottle virus cDNA of this invention. The present pepper mottle virus plant infectious nucleic acid molecule containing the GFP-encoding nucleotide sequence is illustrated in SEQ ID NO:3.

As described in the Examples below, the invention presents a first success of a pepper mottle virus vector enabling to observe the expression of reporter molecule (e.g., GFP) in plants.

Additionally, the vector of this invention may further deliver a foreign gene instead of gene encoding the reporter molecule.

The term “foreign gene” means a gene to be not present in nature plants. The foreign gene may be a modified form of a gene or genes present in other nature plants, an artificially-synthesized form or a fused form of two or more genes. The plants containing these foreign genes may express gene products not to be produced in nature.

To prepare artificially-synthesized genes, DNA synthesis technique and nucleic acid chemical method are used. For instance, the methods described in Gait, M. J. (1985) Oligonucleotide Synthesis: A Practical Approach, IRL Press; Gait, M. J. (1990) Oligonucleotide Synthesis: A Practical Approach, IRL Press; Eckstein, F. (1991) Oligonucleotides and Analogues: A Practical Approach, IRL Press; Adams, R. L. et al., (1992) The Biochemistry of the Nucleic Acids, Chapman & Hall; Shabarova, Z. et al., (1994) Advanced Organic Chemistry of Nucleic Acids, Weinheim; Blackburn, G. M. et al., (1996) Nucleic Acids in Chemistry and Biology, Oxford University Press; and Hermanson, G. T. (1996) Bioconjugate Techniques, Academic Press are utilized, the disclosure of which is herein incorporated by references.

The foreign gene of this invention includes any gene encoding a suitable protein to be massively expressed in plants, for example, peptides with pharmacological efficacies (e.g., interleukin, chemokine, granulocyte macrophage-colony stimulating factor (GM-CSF), macrophage-colony stimulating factor (M-CSF), granulocyte-colony stimulating factor (G-CSF), multi-CSF (IL-3), erythropoietin (EPO), leukemia inhibitory factor (LIF), tumor necrosis factor, interferon, platelet-derived growth factor (PDGF), epithelial growth factor (EGF), fibroblast growth factor (FGF), hematocyte growth factor (HGF) or vascular endothelial growth factor (VEGF)), hormones (e.g., insulin, growth hormone or thyroid-stimulating hormone), vaccine antibodies, blood products, peptides useful in agriculture such as anti-bacteria protein, various enzymes synthesizing secondary metabolites, inhibitors regulating enzyme activity, glycidin of bean lowering blood pressure or enzymes required for process of bioethanol production (e.g., cellulase, hemicellulase or pectinase), but not limited to.

In addition, the present vector includes antibiotics (example: neomycin, carbenicillin, kanamycin, spectinomycin, hygromycin, etc.)-resistant genes (example: neomycin phosphotransferase (nptII), hygromycin phosphotransferase (hpt), etc.) as a selection marker.

In another aspect of this invention, there is provided a cell transformed or infected with the plant infectious nucleic acid molecule or its transcripts, the recombinant vector or its gene as described above.

In still another aspect of this invention, there is provided a plant transformed or infected with the plant infectious nucleic acid molecule or its transcripts, the recombinant vector or its gene as described above.

The preparation of transformed cells and plants of this invention may be carried out using wild-type and mutated pepper mottle virus-derived plant infectious nucleic acid molecule excluded aphid infectivity through site-directed mutagenesis.

To prepare the transformed cells and transgenic plants of this invention, cDNA sequence and its transcripts, preferably cDNA gene may be used.

The method to prepare the transcripts may be carried out according to the methods known to those skilled in the art. Using the recombinant vector, it is preferable to linealize the vector in preparation of transcripts.

To introduce a foreign nucleotide sequence into plants may be performed by the methods (Methods of Enzymology, Vol. 153, 1987, Wu and Grossman Edition, Academic Press; the disclosure is herein incorporated by reference) known to those skilled in the art. The plant may be transformed by using the foreign nucleotide inserted into a carrier (e.g., vectors such as plasmid or virus) or Agrobacterium tumefeciens as a mediator (Chilton et al., Cell, 11: 263-271 (1977); the disclosure is herein incorporated by reference), and by directly inserting the foreign nucleotide into plant cells (Lorz et al., Mol, Genet., 199: 178-182 (1985); the disclosure is herein incorporated by reference). For example, electroporation, microparticle bombardment, polyethylene glycol-mediated uptake may be used in the vector containing no T-DNA region.

The term “plant(s)” is understood by a meaning including a plant cell, a plant tissue and a plant seed as well as a mature plant.

The present transgenic plants preferably comprise the genus Nicotiana and Capsicum and more preferably Nicotiana benthamiana, Nicotiana tabacum and Capsicum annuum.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 schematically represents a flowchart for cloning a full-length PepMoV-Vb1 and screening infectious clones.

FIG. 2 schematically represents a procedure to construct the full-length cDNA copy of PepMoV-Vb1 RNA in the downstream of CaMV 35S promoter. The final plasmid was designated as “p35SPepMoV-Vb1”, representing the complete DNA copy of PepMoV-Vb1 genome.

FIG. 3 represents a procedure to construct pSP6PepMoV-Vb1/GFP. GFP gene was inserted between NIb and CP cistron of pSP6PepMoV-Vb1. A NIb/CP recognition peptide was introduced between NIb and CP.

FIG. 4 represents RT-PCR analysis (A) of mRNA from N. benthamiana infected with pSP6PepMoV-Vb1/GFP and primer positions (B) on viral genome. Specific primers were used to amplify PepMoV-Vb1-CP (˜820 bp) and GFP (˜700 bp). Primers were designed for producing each different PCR fragments in size.

FIG. 5 schematically represents a method to prepare pSP6PepMoV-Vb1/GFP-NAT vector. The base sequences represent sense and antisense primer used in a vector preparation.

FIG. 6 schematically represents a strategy to completely sequence PepMoV-Vb1 genome.

FIG. 7 shows RT-PCR products of PepMoV-Vb1.

FIG. 8 represents phylogenic trees of 15 species of Solanaceae-infectious potyvirus, which is based on the multiple alignments of complete polyprotein (A), P1 (B) and CP sequences (C).

FIG. 9 is a putative full-length RT-PCR product of PepMoV-Vb1 cDNA. Lane M is a ladder; Lane F and arrowhead represent PCR products.

FIG. 10 shows a procedure to construct pSP6PepMoV-Vb1 vector containing a bacteriophage SP6 RNA promoter and RT-PCR products of PepMoV-Vb1. N-PepMoV-Vb, N-terminal RT-PCR products (˜4.4 kb); C-PepMoV-Vb, C-terminal RT-PCR products (˜5.2 kb).

FIG. 11 represents a comparison of RFLP (restriction fragment length polymorphism) patterns of the full-length DNA of pSP6PepMoV-Vb1 based on the nucleotide sequence of PepMoV-Vb1. Upper panel: restriction map, bold horizontal line, full-length cDNA of pSP6PepMoV-Vb1, thin line, pBSSK (−) II vector. Lower panel: RFLP pattern of pSP6PepMoV-Vb1; Lane M, 1 kb⁺ DNA ladder; lane 1, no cut; lane 2, EcoR I; lane3, EcoR V; lane 4, PstI; lane 5, Sac I; lane 6, SalI; lane 7, Xba I; lane 8, XhoI; lane 9, BamH I/Cla I; lane 10, Spe I/SalI.

FIG. 12 represents the comparison of RFLP (restriction fragment length polymorphism) patterns of the putative full-length DNA of p35SPepMoV-Vb1. RT-PCR analysis (A) and primer positions (B) used in restriction mapping or PCR analysis.

FIG. 13 is the photograph of 1% agarose gel representing in vitro transcript product of pSP6PepMoV-Vb1. Lane M, 1 kb⁺ DNA ladder; lane 1, transcripts of SP6PepMoV-Vb1; lane 2, transcripts from putative full-length RT-PCR products.

FIG. 14 shows photographs representing the symptoms in N. benthamiana infected with in vitro transcripts of wild-type PepMoV-Vb and pSP6PepMoV-Vb1 by mechanical inoculation. At 5-14 days post-inoculation, the photographs were taken: A (5 dpi), C and E (10 dpi), PepMoV-Vb/Sap-infected plants; B (5 dpi), D and F (10 dpi), pSP6PepMoV-Vb1-infected plants.

FIG. 15 represents RT-PCR (A) and Western blotting (B) analysis in N. benthamiana infected with pSP6PepMoV-Vb1 clone. Lane 1, leaf extract of plants infected with wild-type PepMoV-Vb; lane 2, healthy plants as negative control; lane 3-9, leaves extracts of plants infected with in vitro transcripts of pSP6PepMoV-Vb1 by mechanical inoculation; lane M, 1 kb⁺ DNA ladder and protein size marker. The experiments were carried out two times.

FIG. 16 shows photographs representing the symptoms in C. annum ECW inoculated with pSP6PepMoV-Vb1. Photographs: A, C, E and G, wild-type PepMoV-Vb/Sap; B, D, F and H, pSP6PepMoV-Vb1/sap.

FIG. 17 represents the results to detect virus-specific genes or proteins in N. benthamiana inoculated with in vitro transcripts of pSP6PepMoV-Vb1. The infectivity of pSP6PepMoV-Vb1 to N. benthamiana were analyzed by RT-PCR using CT primer (A) and VPg-specific primer (B) and by Western blotting with anti-serum against PepMoV-CP. Lane 1, inoculated leaves of plants infected with pSP6PepMoV-Vb1; lane 2, systemic upper leaves of plants infected with pSP6PepMoV-Vb1; lane 3, inoculated leaves of plants infected with PepMoV-Vb/Sap; lane 4, systemic upper leaves of plants infected with PepMoV-Vb/Sap; lane 5, healthy leaves as negative control; lane M, 1 kb⁺ ladder and protein size marker.

FIG. 18 is the photograph of 1% agarose gel representing in vitro transcription products of pSP6PepMoV-Vb1/GFP. Lane M1, 1 kb⁺ ladder (˜100 ng); lane M2, 1 kb⁺ ladder (˜300 ng); i-T, Sac II-linealized pSP6PepMoV-Vb1 templates; i-I, in vitro transcripts of pSP6PepMoV-Vb1; ii-T, Sac II-linealized pSP6PepMoV-Vb1/GFP templates; ii-I, in vitro transcripts of pSP6PepMoV-Vb1/GFP.

FIG. 19 is the photograph visualizing green fluorescent protein (GFP) under UV light in N. benthamiana infected with pSP6PepMoV-Vb1/GFP. The photographs were taken at 4, 5, 7, 10 and 14 days post-inoculation (dpi), respectively.

FIG. 20 is the photograph exhibiting green fluorescence illuminated by GFP under UV light in flower (A) and root (B) of N. benthamiana infected with pSP6PepMoV-Vb1/GFP at 30 dpi.

FIG. 21 represents Western blotting for PepMoV-Vb coat protein of systemically-infected tobacco leaves at 14 dpi. Lane M, protein size marker; lane 1, healthy plants; lane 2, pSP6PepMoV-Vb1-infected plants; lane 3, Ls-CMV-inoculated plant. The position of PepMoV-Vb coat protein is indicated by the arrowhead.

FIG. 22 is the photograph exhibiting green fluorescence in the systemic leaves of pepper infected with pSP6PepMoV-Vb1/GFP. The first true leaves of pepper were inoculated with progeny viruses obtained from N. benthamiana infected with pSP6PepMoV-Vb1/GFP. The photographs in all leaves were taken under UV light at 5 (a, a′, b, b′), 12 (c, c′) and 30 (d, d′, e, e′) dpi, respectively. The photograph (e′) is to magnify the circle-indicated region of d′.

FIG. 23 represents the stability analysis of pPepMoV-Vb1/GFP through passage (P) in the systemically-infected leaves of N. benthamiana. The primers were used in RT-PCR amplification of PepMoV-Vb1-CP and GFP. Lane 1, pSP6PepMoV-Vb1-infected plants at 30 dpi (P0); lane 2, pSP6PepMoV-Vb1/GFP-infected plants at 30 dpi (P0); lane 3-5, pSP6PepMoV-Vb1/GFP-infected plants at 7, 14 and 21 dpi (P1), respectively; lane 6-7, pSP6PepMoV-Vb1/GFP-infected plants at 7 and 14 dpi (P2), respectively.

FIG. 24 is the result to analyze the infectivity of SP6PepMoV-Vb1/GFP-NAT. By analyzing the expression patterns of GFP induced by inoculating the transcripts of SP6PepMoV-Vb1/GFP-NAT and SP6PepMoV-Vb1/GFP into pepper, the infectivity of SP6PepMoV-Vb1/GFP-NAT is similar to that of SP6PepMoV-Vb1/GFP in whole pepper plant as well as leaves and stems of pepper plant.

FIG. 25 represents a system to examine the aphid infectivity of pSP6PepMoV-Vb1/GFP-NAT constructed as a vector for blocking aphid transition. The contamination caused by aphids and inaccuracy of the results were excluded by analyzing an aphid-mediated infectivity in pepper and tobacco plants using a separated cultivation system prepared to determine the exact aphid mediation infectivity.

The present invention will now be described in further detail by examples. It would be obvious to those skilled in the art that these examples are intended to be more concretely illustrative and the scope of the present invention as set forth in the appended claims is not limited to or by the examples.

EXAMPLES Experimental Materials and Methods 1. Sources of Plants

Nicotiana benthamiana was generally used for propagation of PepMoV-Vb1. It could be easily infected with virus sap by mechanical inoculation and full-length clone. For the host range study of pSP6PepMoV-Vb1/GFP, the following plant species were inoculated with progenies of SP6PepMoV-Vb1/GFP, Nicotiana tabacum cv. Xanthi-nc, Samsun NN, Samsun nn, Solanum lycopersicon, Chenopodium amaranticolor, zucchini squash (C. pepo cv. Black Beauty) and pepper plants were grown in a greenhouse of Seoul Women's University in Seoul, Korea. N. benthamiana infected with the SP6PepMoV-Vb1/GFP was ground in 0.01 M phosphate buffer, pH 7.2. The inoculum was applied to leaves of healthy plants dusted with carborundum.

2. Virus Sources

Pepper mottle virus (PepMoV-Vb) used throughout this work was originally isolated from Capsicum annuum L. var. grossum in Hwasung, Kyungki province in Korea. The isolate is available from Plant Virus GenBank, Seoul, Korea (PVGB accession No. PV-0170).

3. Bacterial Strains and Plasmids

Competent Escherichia coli strains were used ABLE K, SURE, XL10-Gold (Stratagene, USA), DH5α and JM109. A full-length clone amplified and maintained in XL10-Gold. The plasmids of pBluescript SK 2(−) (Stratagene, USA) and pGEM T-Easy (Promega, USA) were used for full-length construction and sub-cloning of cDNAs of PepMoV-Vb1.

4. Construction of Full-Length cDNA of PepMoV-Vb1

The work flow for the construction of in vitro- and in vivo infectious full-length cDNA clone of PepMoV-Vb1 was outlined in FIG. 1.

4-1. A Full-Length cDNA Copy of PepMoV-Vb1 RNA with SP6 Promoter

A full-length cDNA copy of PepMoV-Vb1 RNA was synthesized by long template RT-PCR with a primer set of Kpn I-SP6 5′ and polyA-Sac II 3′. Primer used synthesis of cDNAs of PepMoV-Vb1 were listed in Table 1. Reverse transcription PCR(RT-PCR) was performed in 50 μl of reaction volume containing total RNA template, 1× buffer, 0.5 mM dNTP, 1 μM downstream primer, and 10 U SuperScriptII reverse transcriptase. PCR was performed in 50 μl of reaction volume consisting of 1 μl of first strand cDNAs, 1× buffer, 0.5 mM dNTP, 0.75 mM MgCl₂, 0.5 μM of the upstream and the downstream primers, and Expand long template DNA polymerase (Roche). RT-PCR was performed along to cycles of five different annealing temperatures. PCR was performed 4 min at 94° C. followed by five cycle of 20 sec at 94° C., 40 sec at 55° C. and 10 min at 68° C., ten cycles of 20 sec at 94° C., 40 sec at 56° C. and 9 min at 68° C., ten cycles of 20 sec at 94° C., 40 sec at 57° C. and 10 min at 68° C., five cycles of 20 sec at 94° C., 40 sec at 58° C. and 10 min at 68° C. Finally, the mixtures were incubated at 68° C. for 15 min for extension.

TABLE 1 Primer sequences for constructing a full-length PepMoV-Vb1 and Sequencing. Fragment Primers Primer sequence (5′ → 3′) 1 KpnI-SP6 5′ 5′-GAGAGGTACCATTTAGGTGACACTATAG AAATTAAAACATAACATACAA-3′ BamHI 3′ 5′-CCCTTAAATGTTGTCGAG-3′ 2 BamHI 5′ 5′-CTTCAAAATGATTGGATC-3′ PacI 3′ 5′-ATCGAGGGTGAGAGAATG-3′ 3 PacI 5′ 5′-AGTGAGCGAGTTTCATGC-3′ BgIII 3′ 5′-AGTGAGCACACAACACCC-3′ 4 BglII 5′ 5′-AACTGAAGATCTCAAGAA-3′ SpeI 3′ 5′-CCACCTGGCAGAGAGGTGGAG-3′ 5 SpeI 5′ 5′-GGCTTACTCTTTGTTCCTCGTG-3′ ClaI 3′ 5′-TAGCTCTGAGTGCATTTG-3′ 6 ClaI 5′ 5′-TTGCGATCATCATCGATT-3′ NcoI 3′ 5′-CTCAAACAGCTTTGCCGG-3′ 7 NcoI 5′ 5′-CATGCAGATCCATGGCTT-3′ SalI 3′ 5′AATATTTGGGGACGTGCC-3′ 8 SalI 5′ 5′-CTTGAATACAAACCAAGC-3′ polyA- 5′-GGGGTACCT(30)GTCTCTCTCATGC KpnI 3′ CAAC-3′ 4-2. A Full-Length cDNA Copies of PepMoV-Vb1 RNA with CaMV 35S Promoter

The plasmid p35SPepMoV-Vb1 contained the CaMV 35S promoter, the complete PepMoV-Vb1 DNA and poly (A) 30 tract. First, CaMV 35S promoter and 5′ region of PepMoV-Vb1 (1-1393 nt) was fused by PCR with primer sets of Sph I 35S pro 5′ and 35S pro3′ or 35S pro-end 5′ and BamH I PepMoV 3′, and then fusion PCR product (PepMoV-Vb1/5′SphI-BamHI) was dehydrolyzed by Sph I-BamH I. The plasmid pBS/SK2 (−) was modified for use as the backbone in the construction of the 35SPepMoV-Vb1 vector by deletion of the multiple-cloning site except BamH I and Sph I (provided by Prof. I. Uyeda in Hokkaido University; See, Reference). Subsequently, this fragment was introduced into modified pBS/SK2 (−). Next, Kpn I-Nco I-Pst I linker was inserted into BamH I site of pPepMoV-Vb1/SphI-BamHI and the region of Kpn I-Nco I PepMoV-Vb1 (7305-9670 nt contained poly-(A)30) was introduced into pPepMoV-Vb1/5′SphIBamHI-NcoIKpnI3′. Finally, a full-length construct of PepMoV-Vb1 was completed by BamH I-Nco I (1393-7305 nt) region of PepMoV-Vb1 insertion to pPepMoV-Vb1/5′SphIBamHI-NcoIKpnI3′. This clone hereafter referred to as “p35SPepMoV-Vb1” (FIG. 2).

5. Construction of GFP Expression Vector Base on pSP6PepMoV-Vb1

The GFP cDNA was PCR-amplified from turboGFP vector (Evrogen, Russia) and introduced into pSP6PepMoV-Vb1 so that the open reading frame for GFP was placed in-frame between the sequences coding for NIb and CP, generating a recombinant plasmid, pSP6PepMoV-Vb1/GFP. GFP was cloned using primer set of 5′ turboGFP (5′-ATGGAGAGCGACGAGAGC-3′) and 3′ turboGFP (5′-TTCTTCACCGGCATCTGC-3′). A NIa protease cleavage site was introduced between GFP and CP. The primers to construct the pSP6PepMoV-Vb1/GFP are summarized in Table 2.

For pSP6PepMoV-Vb1/GFP, PCR fragments were obtained NIb-GFP, GFP and GFP-CP. The PCR fragments NIb-GFP and GFP-CP are designed overlapped 3′ region of NIb and 5′ region of GFP or overlapped 3′ region of CP and 5′ region of CP, respectively. The DNA fragment of the 3′ region of NIb fused to turboGFP was first amplified with the primer NcoI-5′ and NIbGFP3′ (FIG. 3, A-I) and then, the DNA fragment of the 5′ region of CP fused to NIb::GFP was amplified with the primer pairs of GFPCP 5′ and PepMoV-Sac II 3′ (FIG. 3, A-III). The NIb-GFP and GFP-CP gene were amplified with the primer NcoI-5′ and CP-GFP3′ (FIG. 3, A-I::II) or NcoI-5′ and polyA-SacII3′ (FIG. 3, A-I::II::III), respectively. The GFP gene was amplified with NIbGFP 5′ and GFP-CP3′ (FIG. 3, A-III). Finally, the fusion PCR product was cloned pGEM T-Easy vector (FIG. 3, B). The junctions and the inserted sequences were confirmed by sequencing. The NIb::GFP::CP fragment was cut with EcoN I-Sal I and ligated into EcoN I-Sal I treated pSP6PepMoV-Vb1, creating the recombinant plasmid pSP6PepMoV-Vb1/GFP. The plasmid construct was amplified and maintained in E. coli XL10-Gold as pSP6 PepMoV-Vb1 and hereafter referred to as “PepMoV-Vb1/GFP” (FIG. 3, C).

TABLE 2 Fusion PCR primers to construct SP6PepMoV-Vb1/GFP Fragment Primer Primer sequence I NcoI-5′ 5′-CATGCAGATCCATGGCTT-3′ NIbGFP3′ 5′-CTCGTCGCTCTCCATGCTGCTCTG ATGATGAACTTC-3′ II NIbGFP5′ 5′-GTTCATCAGAGCAGCATGGAGAGC GACGAGAGCGG-3′ CPGFP3′ 5′-GATGAACTTCATATTCTTCACCGG CATCTGCATCCCG-3′ III GFPCP5′ 5′-GATGCCGGTGAAGAATATGAAGTT CATCATCAGAGCAG-3′ polyA- 5′-GAGACCGCGGT15GTCTCTCTCAT GCCAACTACG-3′ SacII3′ I::II Nco I-5′ 5′-CATGCAGATCCATGGCTT-3′ CPGFP3′ 5′-GATGAACTTCATATTCTTCACCGG CATCTGCATCCCG-3′ I::II::III Nco I-5′ 5′-CATGCAGATCCATGGCTT-3′ polyA- 5′-GAGACCGCGG T15GTCTCTCTCA SacII3′ TGCCAACTACG-3′ GFP TurboGFP 5′ 5′-ATGGAGAGCGACGAGAGC-3′ TurboGFP 3′ 5′-TTCTTCACCGGCATCTGC-3′ CP PepMoV- 5′-AGCGCTCAAGCTCAGACAC-3′ CP5′ PepMoV- 5′-CATATTTCTGACCCCAAGCAG-3′ CP3′ VPg PepMoV- 5′-GCTCTAGAGGACGCTCTAAGAC VPg5′ G-3′ PepMoV- 5′-GGGGTACCTTCGTGCTTCACAA VPg5′ C-3′ NAT1 NAT5′ 5′-GAGCAGCTCAAGATCAGACACATTGGA CGCTGAAGAGGAGAAAAAG-3′ NAT2 NAT3′ 5′-GTGGCTACTTCTTTATTTTTCTTTTTC TCCTCTTCAGCGTCCAATGTGTC-3′ 6. Assessments of Infectivity of pSP6PepMoV-Vb1 and pSP6PepMoV-Vb1/GFP 6-1. In vitro Transcription and Infectivity Test

Full-length cDNA clones of the pSP6PepMoV-Vb1 and pSP6PepMoV-Vb1/GFP were used as template for in vitro transcription reaction following plasmid linearization with Sac II. In vitro transcription reactions were carried out in a volume of 50 μl containing 10 mM DTT, 5 mM rATP, 5 mM rCTP, 5 mM rUTP, 0.5 mM rGTP, 0.5 mM cap analog (m7 GpppG), 20 unit of SP6 RNA polymerase, 1 unit RNase inhibitor (TAKARA, Japan) and 1 μg of plasmid DNA linearized with Sac II. After incubation for 15 min at 37° C., 5 μl of 5 mM rGTP was added and incubation was continued for an additional 1 hour. For infectivity test of pSP6PepMoV-Vb1 and pSP6PepMoV-Vb1/GFP, N. benthamiana plants were inoculated in the first expanded leaf when they were 5 weeks old. Inoculations with the in vitro transcripts were derived from pSP6PepMoV-Vb1 and pSP6PepMoV-Vb1/GFP that Sac II linearlized plasmid with SP6 RNA polymerase. More than 5 independent experiments were carried out under the same experimental conditions. Those that developed symptoms were analyzed for accumulation of PepMoV-Vb1-encoded RNA or protein and GFP by RT-PCR, western blot and GFP fluorescent monitoring.

6-2. Reverse Transcription-Polymerase Chain Reaction (RT-PCR)

RT-PCR was performed to confirm PepMoV-Vb1 infection in tested hosts. Total nucleic acids were extracted from infected plant using a phenol/chloroform method were used as templates. RT was performed in a reaction mixture (20 μl) containing 2.5 mM MgCl₂, 0.5 mM of each dNTPs, 1 μl of 50 μM reverse primer, 1× buffer, 1 unit RNase inhibitor, and 2.5 units MuLV reverse transcriptase (Qbiogene, France) at 42° C. for 60 minutes. PCR was performed in a 50 μl of the synthesized cDNA, 1× buffer, 2.5 mM MgCl₂, 0.04 unit Ex-Taq polymerase (TAKARA, Japan), 1 μl of 50 μM reverse and forward primers. To detect the CP, VPg, and inserted entire GFP we used specific primers listed in Table 2, respectively.

To distinguish GFP sequence in the recombinant PepMoV-Vb1 RNA or not, we used the primer pair Nco I 5′ and Sal I 3′ (Table 1). This corresponds to the 3′ region of the NIb cistron (nucleotide 7295-7312) and the 5′ region of the CP cistron (nucleotide 8937-8954) as shown in FIG. 4.

6-3. Western Blot Analysis

For western blot analyses, protein samples were separated on SDS-polyacrylamide gel and transferred onto NC membrane by electro-blotting using an electro transfer unit (Bio-Rad, USA). Membrane was washed three times with TBST buffer (20 mM Tris (pH 7.5), 150 mM NaCl, and 0.1% Tween 20) and blocked for 1 hours with 5% nonfat dried milk. Membrane was probed with antibody (1:1,000 dilutions; immunoglobulin G (IgG) fraction; 1 mg/ml) against PepMoV-CP or turboGFP. Membrane was washed three times in TBS-T buffer and incubated with an alkaline phosphatase (AP)-conjugated secondary antibody (1:7,500 dilution; Promega, USA). Membrane was washed three times with TBST buffer and rinsed once in AP-substrate buffer (0.1 M Tris (pH 9.5), 100 mM NaCl, and 50 mM MgCl₂). To visualize antibody-specific proteins, membrane was reacted with AP-substrate solution (Western Blue Stabilized Substrate Solution, Promega, USA) and the color reaction was terminated with 0.05 M EDTA solution.

6-4. Detection of GFP Fluorescence

Expression of GFP in the inoculated and the upper noninoculated leaves was monitored under illumination with a UV-light and by epifluorescent microscopy (Leica, epifluorescence microscope; Leica, Solms, Germany). The GPF-expressed plants were photographed with a Nikon distal camera (D-70).

7. Analysis of Stability and Passage Experiments of pSP6PepMoV-Vb1/GFP

The stability of pSP6PepMoV-Vb1/GFP was assessed by successive passages of recombinant from systemically infected plant tissues. Recombinant progeny virus in the infected plants of N. benthamiana was mechanically transferred to healthy plants at 7 days intervals. After several passages, the leaves collected from the tested host plants were analyzed by western blotting and RT-PCR with GFP or CP antisera and appropriate primer pairs, respectively. To further monitoring, the possible deletion of viral genome or escape of GFP from pSP6PepMoV-Vb1/GFP and RT-PCR analysis from its progeny-infected hosts was performed by PCR with specific primers.

8. Construction of NAT (Non-Aphid Transmission) Vector based on pSP6PepMoV-Vb1/GFP

For pSP6PepMoV-Vb1/GFP-NAT, the induction of mutation in the particular region was performed according to mutagenesis induction kit (Stratagene, USA). After PCR using NAT5′ and NAT3′ primers, and pSP6PepMoV-Vb1/GFP as a template, the PCR products were digested with Dpn I. Non-mutated templates were removed and then transformed into E. coli strain, XL1-Blue. By sequence analysis, it is confirmed to substitute E for G in the DAG region and then the region amplified with NcoI-5′ and polyA-Sac 113′ primers was cloned into pGEM T-Easy vector to exclude infectivity loss or other problems caused from PCR errors in the resulting pSP6PepMoV-Vb1/GFP-NAT. The clone was sequenced and then inserted into pSP6PepMoV-Vb1/GFP restricted with EcoN I-Sal I, generating a pSP6PepMoV-Vb1/GFP-NAT. The plasmid construct was amplified and maintained in E. coli XL10-Gold and hereafter designated as a “PepMoV-Vb1/GFP-NAT” (FIG. 5).

9. Aphid Infectivity Analysis

The procedures to grow and manipulate aphids and to analyze the plants were performed according to a conventional method (Atreya, D. D., Raccah, B. and Pirone, T. P. Virology 178:161-165 (1990)). Virus-mediated infectivity experiments were carried out using wingless adult insects of Aphis gossypii and Myzus persicae. To compare aphid-mediated invasion, the aphids were separated from the plants for 2 hrs before inoculation and suck juices for 15 min in pepper and tabacum plants infected with pSP6PepMoV-Vb1/GFP-NAT transcripts (acquisition access period). Thus, the aphids were collected and transferred to the healthy plants, following the inoculation for 1 hr (inoculation access period). A separated cultivation system was used to obtain the contamination of the aphids and exact results and plants were observed in the incubation room (FIG. 25).

Results 1. Complete Nucleotide Sequencing of PepMoV-Vb1

To construct infectious full-length cDNA clone of PepMoV-Vb, the PepMoV-Vb genome divided into overlapped segments contained unique restriction enzyme site by RT-PCR as shown in FIG. 6. Eight PCR products were synthesized representing essentially the entire genome and each PCR product subsequently cloned into the pGEM-T Easy vector system (Promega, U.S.A.) (FIG. 7). Each clone was sequenced and full genome RNA sequences of PepMoV-Vb was assembled based on PepMoV-Vb sequence. All primers were also designed based on PepMoV-Vb sequence (GenBank/EMBL/DDBJ accession No.AB126033). The complete nucleotide sequence of PCR fragments was not identical to PepMoV-Vb. Hereafter we renamed assembled full-length PepMoV-Vb to PepMoV-Vb1. The oligonucleotide primers used to synthesize the PCR products and sequencing of cDNA clones were listed in Table 1.

The genome of PepMoV-Vb1 consists of 9,640 nucleotides long contained an extra guanosine residue at the 5′ terminus and 3′ end following a poly (A) 15 tract. The genome RNA encodes a single large ORF coding for polyprotein of 349 kDa (3068 aa), which is the typical genome structure of the potyviruses. The ORF start with an AUG start codon at position 168 to 170 and end with the termination codon UGA at position 9372 to 9374. The 5′- and 3′ NTR was consisted of 168 nucleotides and 267 nucleotides, respectively. The 5′NTR of PepMoV-Vb1 was present two conserved blocks of sequences which are referred to as box ‘a’ and ‘b’ in potyvirus. Box a (AUACAACAU) and b (UCAAGCAU) was detected from the 5′ end in PepMoV-Vb1. These sequences and their secondary structure may be important for processes such as encapsidation, translation or replication (Riechmann et al., 1992)

PepMoV-Vb1 has nine sequences of the potential cleavage site and the genome organizations of PepMoV-Vb1 are shown in Table 3.

TABLE 3 Amino acid sequences present in the amino acid residue of the potential cleavage site of PepMoV-Vb1 polyprotein and adjacent to the cleavage site Connection Amino acid position site P6 P5 P4 P3 P2 P1 P′1 P′2 P′3 Protease P1/HC-Pro L H M E Q Y S T S P1-Pro HC-Pro/P3 K H Y R V G G T V HC-Pro P3/6K1 K Q V I H Q R S T NIa-Pro 6K1/CI S E V R H Q S L D NIa-Pro CI/6K2 Q F V H H Q S K S NIa-Pro 6K2/VPg S E V S H Q G R S NIa-Pro VPg/NIa E V V K H E A K T NIa-Pro NIa/NIb E C V R E Q A H T NIa-Pro NIb/CP Y E V H H Q S S S NIa-Pro

The cleavage site at C-terminal of P1 occurs probably at the dipetide Y/S (287-288 aa) and HC-Pro/P3 cleavage site also occurs at G/G dipeptide (743-744 aa). The remaining seven protease recognition sites are putatively cleaved by the NIa-Pro at dipeptide Q/R (1104-1105 aa), Q/S (1156-1157, 1790-1791, 2795-2796 aa), E/A (2030-2031 aa), Q/G (1842-1843 aa) and Q/A (2276-2277 aa), which are also found in other potyvirus genomes. All of these cleavage sites for PepMoV-Vb1 showed identical to those of other known PepMoV isolates.

In addition, several conserved amino acid residues organized in functional motif of potyviruses were detected in the PepMoV-Vb1 polyprotein. The FIVRG motif (259-263 aa) of PI genome was reported proteolytic domain. The CCCTT motif (577-581 aa) and LAIGN motif (533-537 aa) were present in HC-Pro of PepMoV-Vb1 probably involved in the viral long distance movement and cell to cell movement respectively. The conserved nucleotide-binding motif VGSGKST (1243-1249 aa) and the RNA helicase motif DECH (1330-1333 aa) were found in the CI of the genome. The conserved RNA-dependent RNA polymerase motif of positive-stranded viruses, CDADGS (2521-2526 aa) and SGC35X3NTX30GDD (2586-2629 aa), were found in the NIb of the genome. Motifs known to be involved in the aphid transmission KLTC (337-340aa), PTK (595-597 aa), FRNK (466-469 aa) and DAG (2804-2896 aa) could be found in the HC-Pro and CP of PepMoV-Vb1. The CP cistron also contained an amino acid motif, RX43D (2958-3002 aa) that was required for viral long distance movement.

2. Sequence Alignments and Phylogenetic Analyses of PepMoV-Vb1

The complete sequence of PepMoV-Vb1 showed high sequence identity with other PepMoV isolates, PepMoV-Vb (99.3%), PepMoV-C (94.9%) and PepMoV-FL (94.0%), at the nucleotide level. PepMoV-Vb1 polyprotein amino acid sequence identity with PepMoV-Vb (98.7%), PepMoV-C (95.8%) and PepMoV-FL (95.9%) isolate. Table 4 shows percentages amino acid identity of PepMoV-Vb1 functional proteins compared to the corresponding proteins of some potyvirus members infecting Solanaceous species. Amino acid identity of the entire PepMoV-Vb with PepMoV isolates ranged from 98.7% (Vb1) to 95.8% (PepMoV-C), and with other some potyvirus, from 66.8% (PTV) to 44.1% (ChiVMV and PSbMV).

The multiple alignments of the deduced amino acid sequences showed that P1 is highly variable. The highest identity was found within isolates of PepMoV, Vb (93.7%), C (87.8%) and FL (85.0%), while the percentage identity with other potyviruses range from 13.5% with PSbMV to 35.1% with PTV. PepMoV-Vb1 CP revealed the highest identity on the amino acid with the isolate Vb (99.3%), C (98.2%), FL (97.1%) followed by ChiVMV, PTV and PVY. The overall identity between PepMoV-Vb1-CP was lowest with the CP of TVMV (55.9%). P1 and N-terminal region of the CP protein is variable potyviral protein, both in length and amino acid sequence.

TABLE 4 Sequence homology between PepMoV-Vb1 and Solanaceae plant- infectious potyviruses NIa- Poly Virus P1 HC-Pro P3 6K1 CI 6K2 VPg Pro NIb CP protein ChiVMV 14.7 46.9 19.4 38.5 49.6 52.0 50.0 46.9 58.5 73.4 44.1 PepMoV- 93.7 98.2 99.2 100.0 98.9 100 99.5 98.8 99.2 99.3 98.7 Vb PepMoV-C 87.8 97.4 96.6 98.1 97.3 98.0 96.3 97.6 91.8 98.2 95.8 PepMoV- 85.0 94.2 96.4 98.1 98.4 100.0 94.1 97.6 97.1 97.1 95.9 FL PepSMV 25.4 61.6 32.8 63.5 68.1 62.7 71.3 70.0 75.5 72.0 60.6 PSbMV 13.5 45.6 18.2 34.6 52.9 37.3 48.6 43.8 59.4 57.4 44.1 PTV 35.1 66.1 40.7 76.9 76.5 66.7 79.8 75.1 78.4 73.4 66.8 PVA 24.4 47.6 25.5 38.5 53.3 39.2 48.7 51.2 58.0 57.9 46.6 PVMV 17.5 47.9 20.0 40.4 51.3 52.9 49.5 50.6 59.9 60.5 45.6 PVV 34.4 59.3 42.4 78.8 76.7 68.6 78.7 71.4 77.9 69.7 65.5 PVY 32.7 63.7 34.4 67.3 69.8 54.9 69.1 65.0 73.4 74.3 61.4 TEV 18.7 47.0 27.3 48.1 55.1 49.0 53.2 47.4 60.0 60.2 46.8 TVMV 22.9 46.7 24.1 51.9 52.9 39.2 45.3 43.8 63.7 55.9 46.3 WPMV 40.0 65.2 43.8 76.9 74.4 68.6 80.3 71.8 77.9 73.4 66.7

To understand evolution trees and a phylogenetic relationship of PepMoV-Vb1, the amino acid sequences of the ten mature functional proteins of P1, CP and entire polyportein were compared with other potyviruses infecting Solanaceae plants. PepMoV-Vb1 showed high homology with previously reported other strains of PepMoV-Vb, PepMoV-C and PepMoV-FL. Therefore, PepMoV-Vb1 isolate was grouped with PepMoV-Vb, PepMoV-C and PepMoV-FL (FIG. 8).

3. Cloning of Full-Length cDNA of PepMoV-Vb1

To generate infectious full-length cDNA clone, we performed RT-PCR using primer set of KpnI-SP6 5′ and polyA-Sac II 3′. Although we was amplified a full-length cDNA copy of PepMoV-Vb about 9.6 kb by long template RT-PCR system successfully (FIG. 9), directed cloning of putative full-length PCR product was laborious. Hence, strategy was designed to avoid toxicity of the viral genome. The procedure of the construction of a full-length cDNA clone of PepMoV-Vb1 with the SP6 RNA promoter is outlined in FIG. 4. The pSP6PepMoV-Vb1 was based on the genome of PepMoV-Vb1. The PepMoV-Vb1 genome was split in two parts using unique enzyme site within the CI cistron. The unique Spe I restriction enzyme site in the CI region permitted the joining of overlapped two parts of PepMoV-Vb1 by sub-cloning. The former researchers of the present inventors already obtained the partial clone (pPepMoV-Vb1-N) from the 5′ region included the SP6 RNA promoter extended to position 4531 in viral genome. The overlapping C-terminus PepMoV-Vb1 fragment was amplified from the first strand cDNA with primer pair of Spe 15′ and polyA-Sac II 3′ (Table 1). The C-terminal RT-PCR fragment of PepMoV-Vb1 introduced into pPepMoV-Vb1-N using Spe I and Sac II restriction enzyme sites. Finally, a full-length cDNA clone of PepMoV-Vb1 with a poly (A) tail of 15 residues was constructed by ligating the Spe I-Sac II RT-PCR fragment (4437-9640 nt of PepMoV-Vb1) with Spe I-Sac II digested pSKPepMoV-Vb-N containing 1-4437 of PepMoV-Vb genome preceded by SP6 RNA promoter (FIG. 10). The present inventors hereafter designated the full-length cDNA clone of PepMoV-Vb1 regulated by SP6 RNA promoter as “pSP6PepMoV-Vb1”. RFLP analysis was performed with pPepMoV-Vb1 by restriction enzymes, BamH I, Cla I, EcoR V, Pst I, Sac I, Sal I, Spe I, Xba I and Xho I. The RFLP patterns of full-length clone were identical to those complete nucleotide sequence for PepMoV-Vb1 (FIG. 11).

Based on the sequence information a strategy was made for assembly of a clone under 35S promoter (FIG. 6). FIG. 6 shows the construction of the plasmid containing the full-length cDNA clone was placed under the control of the CaMV 35S promoter. We hereafter full-length cDNA clone of PepMoV-Vb1 regulate by CaMV 35S promoter referred to p35SPepMoV-Vb1. RFLP analysis was also performed with p35SPepMoV-Vb1 by restriction enzymes, SphI/Pst I, EcoR V and Pst I. The RFLP patterns of full-length clone was identical to those complete nucleotide sequence for PepMoV-Vb1. And RT-PCR was conducted to confirm of p35SPepMoV-Vb1 with specific pair of primer 35S pro 5′ and BamH 13′ (FIG. 12). The infectivity of the putative ten selected constructs was tested in N. benthamiana by mechanical inoculation. The plasmid p35SpepMoV-Vb1 did not infect any of N. benthamiana plants by manual mechanical inoculation. It was repeated the manual inoculation ten times on more than 20 N. benthamiana plants, but still no infectivity was noticed.

4. Infectivity Assay of In Vitro Infectious SP6PepMoV-Vb1 Clone

To analyze infectivity of SP6PepMoV-Vb1clone, Sac II-cut full-length cDNA clone was used as templates for in vitro transcription. Capped in vitro transcripts generated pPepMoV-Vb1 and putative full-length PCR product of PepMoV-Vb1 were infected onto N. benthamiana using mechanically inoculation method (FIG. 13). pPepMoV-Vb1 full-length clone was systemically infectious when inoculated onto N. benthamiana, whereas PCR directed in vitro transcript was not infectious onto N. benthamiana. Symptoms induced 3-5 dpi (days post-inoculation; depending on greenhouse conditions) slight faster (1 or 2 days) than initiation of infection with PepMoV-Vb/Sap. The initial symptom of inoculated N. benthamiana with SP6PepMoV-Vb1 showed severe vein clearing in upper leaves at 4 dpi. No significant symptom differences between pSP6PepMoV-Vb1 and PepMoV-Vb in upper leaves of N. benthamiana were observed. In vitro transcripts of PepMoV-Vb1 were able to develop typical vein banding, severe mosaic symptom, leaf malformation, leaf distortion and yellowing on N. benthamiana (FIG. 14).

5. Confirmation of Infectivity of SP6PepMoV-Vb1 Clone

To confirm infectivity of pSP6PepMoV-Vb1, in vitro transcription of pSP6PepMoV-Vb1 was repeated several times and each transcript was inoculated onto N. benthamiana plants. pSP6PepMoV-Vb1 inoculated N. benthamiana plants were analyzed by RT-PCR (FIG. 15A) and Western blot (FIG. 15B) with PepMoV-CP specific primer and antiserum against PepMoV-Vb to confirm infection of the virus, respectively. RT-PCR product and protein corresponding to the expected size of PepMoV-CP were detected in extracted samples from the pSP6PepMoV-Vb1-infected leaf tissues. No signal was detected in samples from Mock treated plants (FIG. 15).

In addition, N. benthamiana plants showing symptoms of viral infection after inoculation with in vitro transcript of SP6PepMoV-Vb1 was used as a source of inocula to inoculate new sets of N. benthamiana and pepper plants. In order to confirm that the infectivity of pSP6PepMoV-Vb1 in pepper plants, the crude sap from leaf tissues of infected N. benthamiana inoculated onto ECW pepper. Typical symptoms of PepMoV-Vb infection appeared on plants of N. benthamiana as well as pepper plants inoculated with crude sap derived from SP6PepMoV-Vb1 at 3 and 4 dpi respectively. They were showed severe mosaic and malformation symptom to the upper leaves of peppers about 12 days after inoculation (FIG. 15B). In pepper plants, the virus produced typical mottle, severe mosaic symptoms and leaf distortion (FIGS. 16D, 16F and 16H). This test repeated the inoculation several times on more than five N, benthamiana plants, and still infectivity of SP6PepMoV-Vb1 was highly infectious. All plants were analyzed by RT-PCR with specific primer pairs of PepMoV-CP (FIG. 17A) or PepMoV-VPg (FIG. 17B) and western blot with antiserum against PepMoV-Vb to confirm infection of the virus in virus inoculated leaves and noninoculated upper leaves of N. benthamiana. By immunoblotting analysis, a 30 kDa protein corresponding to the CP of PepMoV was detected in the plants infected by the in vitro transcripts derived from SP6PepMoV-Vb1 (FIG. 17C). This is the first report on infectious full-length cDNA cloning of PepMoV isolated from pepper plants.

6. Construction of the a Novel Viral Vector Based on SP6PepMoV-Vb1 Genome

A highly infectious cDNA clone of SP6PepMoV-Vb1 was applied as a viral vector. The pSP6PepMoV-Vb1/GFP was based on the genome of PepMoV-Vb1. A schematic diagram of construct made is shown FIG. 3. The GFP gene (turboGFP) encoding green fluorescent protein was inserted between the cistrons for NIb and CP in pSP6PepMoV-Vb1 by two-step fusion PCR. The inserted GFP in the polyprotein was flanked by the proteolytic cleavage sites recognized by the viral NIa proteinase (YEVHHQ/SS). Finally, the fusion PCR product was cloned pGEM T-Easy vector (FIG. 3B). The NIb::GFP::CP fragment of two-step fusion PCR product was dehydrolyzed with EcoN I-Sal I and ligated into EcoN I-Sal I treated pSP6PepMoV-Vb1, creating the recombinant plasmid pSP6PepMoV-Vb1/GFP.

7. Infection of N. benthamiana with pSP6PepMoV-Vb1/GFP and Systemic Expression of the GFP Gene

Sac II-treated full-length cDNA clone inserted GFP gene, pSP6PepMoV-Vb1/GFP, was used as template for in vitro transcription as same method applied pSP6PepMoV-Vb1 in the present invention. In vitro generated transcripts of pSP6PepMoV-Vb1/GFP and pSP6PepMoV-Vb1 were inoculated onto N. benthamiana plants (FIG. 18). The inoculated N. benthamiana plants could detect systemically infected to PepMoV-Vb1/GFP through GFP fluorescent at 4 dpi (FIG. 19). While there was no green fluorescence in leaves infected with the pSP6PepMoV-Vb1. Symptoms were the similar as those induced by pSP6PepMoV-Vb1. This result indicated that pSP6PepMoV-Vb1/GFP was also as infectious as pSP6PepMoV-Vb1. The systemically infected leaves displayed severe mosaic symptoms and leaves malformation (FIG. 19). In addition, under UV irradiation, green fluorescence signal could be detected before virus symptom was emerged from infected plants of PepMoV-Vb1/GFP at 3 dpi. Subsequently, fluorescent area enlarged and saturated whole plant along the vein (FIG. 19). The GFP expression could detect faster than virus visual symptom emergence in infected plants by PepMoV-Vb1/GFP. The GFP fluorescence also was observed at root tissue as well as flower of N. benthamiana (FIG. 20). To assess the GFP insertion in the symptomatic tissues was confirmed by RT-PCR of the RNA from progeny viruses isolated from the systemically infected upper leaves, and subjected to RT-PCR with three different primer sets to detect the PepMoV-CP, GFP and GFP sequence in the recombinant PepMoV-Vb1 RNA. PCR products of the expected size were detected, suggesting stable preservation of GFP sequence in recombinant viral genome (FIG. 4). The leaves of N. benthamiana systemically infected with PepMoV-Vb1/GFP were performed western blot analyses using an anti-PepMoV-Vb-CP and anti-turboGFP (avrogen) results showed that GFP have been precisely excised from the viral polyprotein with the viral proteases NIa (FIG. 21)

8. Host Range Study of pSP6PepMoV-Vb1/GFP

To determine the host range of PepMoV-Vb1/GFP, infectivity of pSP6PepMoV-Vb1/GFP was assayed by mechanical inoculation onto several plants including plants of C. amaranticolor, Solanum lycopersicon, N. tabacum cv. Xanthinc, N. tabacum cv. Samsun NN, N. tabacum cv. Samsun nn and Capsicum annuum. Plants inoculated with progeny derived from pSP6PepMoV-Vb1/GFP. Pepper plants (C. annuum L.) inoculated with PepMoV-Vb1/GFP progeny derived from pSP6PepMoV-Vb1/GFP infected plant. chlorotic fluorescent lesions were showed in inoculated first true leave at 3 dpi. The pSP6PepMoV-Vb1/GFP induced local circular fluorescence sign on inoculation leaves of the systemic host pepper plant at 3 dpi. The fluorescence moved to downward of stem and then these signals spread toward upper leaf veins along the stem and petiole. Gradually, local florescence induced by initial infection of PepMoV-Vb1/GFP developed to upper leaves under the UV light spread to upper leaves systemically. Finally, GFP fluorescence induced by the pSP6PepMoV-Vb1/GFP developed to whole plant systemically. During systemic spreading of GFP signs, local circular fluorescence still could be detected in infection leaves. The pSP6PepMoV-Vb1/GFP also can be employed as a host system for generating viral progeny by initial inoculation for subsequent experiments with other hosts. These circular fluorescent sign has been spread along the leaf veins (Table 5).

TABLE 5 Host ranges and symptomatological analyses of SP6PepMoV-Vb1/GFP Symptom Inoculated leaves Upper leaves Visible Visible Plant species symptoms fluorescence symptoms fluorescence Nicotiana benthamiana — — sM, Mal, VB SF N. tabacum cv. Xanthi-nc — CSF mM SF, CSF N. tabacum cv. Samsun NN — CSF mM SF, CSF N. tabacum cv. Samsun nn — CSF mM SF, CSF Capsicum annuum L. P915 CSF sM, Mal SF Capsicum annuum ECW CSF sM, Mal SF Capsicum annuum Avelar — — — — Solanum lycopersicon — — — — Chenopodium amaranticolor — — — — C. pepo cv. Black Beauty — — — — Abbreviation: mM, mild mosaic; sM, severe mosaic; Y, yellow; Mal, malformation; VB, vein bending; CSF, circular systemic fluorescence; SF, systemic fluorescence; —, non-infected. 9. Analysis of Stability and Passage Experiments of pSP6PepMoV-Vb1/GFP

To monitor the genetic stability of vector carrying inserted GFP gene in more detail and to understand the structural fate of GFP in active PepMoV-Vb1 recombinants, RT-PCR analyses were carried out on host plants, after initial infection and also after several successive passages. The stability of pSP6PepMoV-Vb1/GFP was verified with time after initial infection and after every successive trans-inoculation of active viral progeny on new individual hosts. PepMoV-Vb1/GFP progeny were passaged through N. benthamiana more than 3 times by mechanical inoculation at 7 days interval until one month. For each passage, the existence and stability of the recombinant virus were monitored using green fluorescence and RT-PCR In the plants of N. benthamiana, inoculated with the SP6PepMoV-Vb1/GFP progeny, severe mosaic and leaf malformation symptoms were consistently observed on young leaves. These symptoms were similar with those of the plants showing symptoms with the SP6PepMoV-Vb1. Inserted GFP was stable in SP6PepMoV-Vb1-based vector for at least 30 dpi (FIG. 23). No observed difference in the appearance of symptoms and those were as severe as for the wild-type virus. Furthermore, we did not notice any difference in expression level and stability at either insertion points.

During the test not detected any deletion or escape of foreign gene so far, the pSP6PepMoV/GFP is expected very stable until end of plant life. Thus, the incorporation of GFP in the viral genome did not affect the ability of PepMoV-Vb1 to infect plants. This is the first developed the PepMoV viral vector to look at the expression of GFP.

10. Analysis of Stability and Passage Experiments of pSP6PepMoV-Vb1/GFP

In vitro transcription was performed using Sac II-restricted SP6PepMoV-Vb1/GFP-NAT as a template and the resulting transcripts were inoculated in N. benthamiana. To comparatively analyze the expression of the present SP6PepMoV-Vb1/GFP and symptoms, and aphid transition, the transcripts using SP6PepMoV-Vb1/GFP constructs were also inoculated and analyzed in N. benthamiana (FIG. 24).

By detecting GFP expression and symptoms in a naked eye, N. benthamiana plants inoculated with SP6PepMoV-Vb1/GFP-NAT were same to the symptoms of those inoculated with SP6PepMoV-Vb1/GFP. In addition, GFP expression was highly expressed in leaves and stems and systemically spread by moving to upper leaves. These results suggested that the novel-designed SP6PepMoV-Vb1/GFP-NAT possesses an infectivity to be useful as a virus vector and a capability to express the foreign gene, GFP.

11. Detection Analysis of Aphid infectivity to pSP6PepMoV-Vb1/GFP-NAT Vector

To examine the infectivity transition of SP6PepMoV-Vb1/GFP-NAT by aphids, virus-mediated detection experiments were carried out in N. benthamiana infected with SP6PepMoV-Vb1/GFP-NAT using wingless adult insects of Aphis gossypii and Myzus persicae. The expression of GFP (a reporter protein) mediated by aphid was tested, resulting in no expression of GFP by aphid mediation. It could be appreciated that the present SP6PepMoV-Vb1/GFP-NAT vector exhibits a possibility to exclude aphid-mediated problems and has a high value to be practically applied as a plant virus vector.

The present invention was supported by the grants from Biogreen21 program of Rural Development Administration (project number: 20070301034010), Plant Signal Transduction Network Center of Korea Science and Engineering Foundation (project number: R11-2003-008-02002-0) and Biogreen21 program of Rural Development Administration (project number: 200804010340550080200).

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Having described a preferred embodiment of the present invention, it is to be understood that variants and modifications thereof falling within the spirit of the invention may become apparent to those skilled in this art, and the scope of this invention is to be determined by appended claims and their equivalents. 

1. A pepper mottle virus-derived plant infectious nucleic acid molecule comprising the nucleotide sequence spanning nucleotides 168 to 9371 of SEQ ID NO:1.
 2. The nucleic acid molecule according to claim 1, wherein the nucleic acid molecule further comprises the nucleotide sequence spanning nucleotides 1 to 167 of SEQ ID NO:1.
 3. The nucleic acid molecule according to claim 1, wherein the nucleic acid molecule further comprises the nucleotide sequence spanning nucleotides 9372 to 9655 of SEQ ID NO:1.
 4. A pepper mottle virus-derived plant infectious nucleic acid molecule comprising the nucleotide sequence spanning nucleotides 168 to 9371 of SEQ ID NO:1, except that the nucleic acid molecule has a substituted nucleotide at nucleotide 9304 of SEQ ID NO:1 to remove aphid-mediated infectivity, in which the substituted nucleotide at nucleotide 9304 is a nucleotide containing A, C or T base.
 5. A recombinant vector, comprising (i) the nucleotide sequence according to claim 1, and (ii) a promoter operatively linked to the nucleotide sequence.
 6. The recombinant vector according to claim 5, wherein the promoter comprises SP6 promoter, T7 promoter, T3 promoter, PM promoter, maize-ubiquitin promoter, Cauliflower mosaic virus (CaMV)-35S promoter, Nopalin synthase (nos) promoter, Figwort mosaic virus 35S promoter, Sugarcane bacilliform virus promoter, commelina yellow mottle virus promoter, photo-inducible promoter of small subunit of Ribulose-1,5-bis-phosphate carboxylase (ssRUBISCO), cytosolic triosphosphate isomerase (TPI) promoter in rice, adenine phosphoribosyltransferase (APRT) or octopine synthase promoter in Arabidopsis.
 7. The recombinant vector according to claim 6, wherein the promoter is SP6 promoter.
 8. The recombinant vector according to claim 5, wherein the vector further comprises a foreign gene.
 9. The recombinant vector according to claim 8, wherein the foreign gene comprises the nucleotide sequence encoding green fluorescent protein (GFP), yellow fluorescent protein (YFP), red fluorescent protein (RFP), GFP-derived variant protein, luciferase, β-glucuronidase, interleukin, chemokine, granulocyte macrophage-colony stimulating factor (GM-CSF), macrophage-colony stimulating factor (M-CSF), granulocyte-colony stimulating factor (G-CSF), multi-CSF (IL-3), erythropoietin (EPO), leukemia inhibitory factor (LIF), tumor necrosis factor, interferon, platelet-derived growth factor (PDGF), epithelial growth factor (EGF), fibroblast growth factor (FGF), hematocyte growth factor (HGF), vascular endothelial growth factor (VEGF), cellulase, hemicellulase or pectinase.
 10. A cell transformed or infected with the plant infectious nucleic acid molecule according to claim 1 or its transcript.
 11. A plant transformed or infected with the plant infectious nucleic acid molecule according to claim 1 or its transcript. 